8FIK

APOBEC3A E72A inactive mutant in complex with ATTC-hairpin DNA substrate

PDB DOI: https://doi.org/10.2210/pdb8FIK/pdb
NAKB: 8FIK

Classification: DNA BINDING PROTEIN/DNA
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2022-12-16 Released: 2023-09-06
Deposition Author(s): Harjes, S., Jameson, G.B., Harjes, E., Filichev, V.V., Kurup, H.M.
Funding Organization(s): Health Research Council (HRC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.91 Å
R-Value Free: 0.232
R-Value Work: 0.200

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

DNA-based inhibitors restrict mutagenic activity of APOBEC3 in cells

Harjes, S., Kurup, H.M., Filichev, V., Harjes, E., Jameson, G.B.

To be published.

Macromolecule Content

Total Structure Weight: 56.86 kDa
Atom Count: 3,937
Modelled Residue Count: 404
Deposited Residue Count: 430
Unique protein chains: 1
Unique nucleic acid chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA dC->dU-editing enzyme APOBEC-3A	A, B	199	Homo sapiens	Mutation(s): 1 Gene Names: APOBEC3A EC: 3.5.4.38
UniProt & NIH Common Fund Data Resources
Find proteins for P31941 (Homo sapiens) Explore P31941 Go to UniProtKB: P31941
PHAROS: P31941 GTEx: ENSG00000128383
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P31941
Sequence Annotations Expand
Reference Sequence

Find similar nucleic acids by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(PCPCPCPAPTPCPAPTPTPCPGPAPTPGPGPG)-3')	C [auth D], D [auth H]	16	Homo sapiens
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
IHP (Subject of Investigation/LOI) Query on IHP Download Ideal Coordinates CCD File SDF format, chain H [auth A] MOL2 format, chain H [auth A]	H [auth A]	INOSITOL HEXAKISPHOSPHATE C₆ H₁₈ O₂₄ P₆ IMQLKJBTEOYOSI-GPIVLXJGSA-N		Interactions Focus chain H [auth A] Interactions & Density Focus chain H [auth A]
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain K [auth B] SDF format, chain L [auth B] MOL2 format, chain G [auth A] MOL2 format, chain K [auth B] MOL2 format, chain L [auth B]	G [auth A], K [auth B], L [auth B]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain G [auth A] Focus chain K [auth B] Focus chain L [auth B] Interactions & Density Focus chain G [auth A] Focus chain K [auth B] Focus chain L [auth B]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain I [auth B] MOL2 format, chain E [auth A] MOL2 format, chain I [auth B]	E [auth A], I [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain I [auth B] Interactions & Density Focus chain E [auth A] Focus chain I [auth B]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain J [auth B] MOL2 format, chain F [auth A] MOL2 format, chain J [auth B]	F [auth A], J [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain F [auth A] Focus chain J [auth B] Interactions & Density Focus chain F [auth A] Focus chain J [auth B]